An apparatus and method is described for dynamically aligning clocks in independent clock domains with minimal latency. In the preferred embodiments, a reference clock in the destination clock domain that is some multiple times the data clock of the destination clock domain is used to sample a data sample signal from the source domain. The sampled data is used to determine at what time slice of the reference clock the data sample signal is changing and therefore at what phase of time slice or phase of the data clock the clocks can be aligned to ensure valid data will be transferred between clock domains.